This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The cell division cycle of the budding yeast Saccharomyces cerevisiae is mainly driven by one Cdk (Cyclin-Dependent Kinase), which becomes active when bound to one of nine cyclin subunits. The majority of the specific associates and substrates for these cyclin-Cdk complexes remain elusive, though their elucidation is essential for a full understanding of the cell cycle. Here we report the results of a targeted proteomics study that identified numerous proteins associated with particular cyclin-Cdk complexes. These included phosphorylation substrates, proteins involved in the ubiquitination-degradation pathway, adaptor proteins and inhibitors. We investigated and confirmed the specificity and biological relevance of some of these interactions. We demonstrate that this approach for studying protein associations within a biological module allowed the detection of many new associations. Our data includes many associations that were missed in previous proteome-wide studies, and shows that even transient and dynamic interactions can be detected by mass spectrometry-based targeted proteomic approaches. This work was presented in Archambault V, Chang EJ, Drapkin BJ, Cross FR, Chait BT, Rout MP, Targeted proteomic study of the cyclin-Cdk module Mol Cell. 2004, 14, 699-711. We are currently gearing up to redoing this experiment under conditions that have been highly optimized over the past several years. Under these new conditions, we hope to isolate &identify a large number of new substrates of Cdk.